A Marin Superior Court judge has ruled the Drakes Bay Oyster Co. must clean up parts of its operation per a California Coastal Commission edict, but it will continue to operate until a federal court decides the farm's fate.

In February the commission unanimously approved cease-and-desist and restoration orders against the oyster company, operated by Kevin Lunny, citing several violations of the state's Coastal Act.

In particular, the commission noted discharging of marine debris; operation of offshore aquaculture facilities; construction, installation and alteration of structures; and land alterations in conflict with the state act.

On Wednesday, Judge Lynn Duryee ruled that elements of the commission's order will be imposed. That will require Drakes Bay to address invasive Manila clams on its property, manage its invasive sea squirts — which have been dubbed "marine vomit" — and clean up the company's plastic debris.

The judge didn't impose the more drastic measures, which would have forced Drakes Bay to remove its oysters and racks, pending the outcome of federal litigation on a larger issue surrounding a federal decision last November not to offer a lease to allow the operation to continue.

The 9th U.S. Circuit Court of Appeals is expected to issue a ruling in the coming weeks on that issue.